Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
fXiibfXiiba fXii surface activation Membrane0 MassAction
fXiiba+fXiibafXiiba+fXiib fXii autoinhibition Membrane0 MassAction
fXiifXiib fXii binding Membrane0 MassAction
fXiibafXiia fXiai release Membrane0 MassAction

fXii surface activation Universal ID's

fXii surface activation Text Annotations

fXii autoinhibition Universal ID's

fXii autoinhibition Text Annotations

fXii binding Universal ID's

fXii binding Text Annotations

fXiai release Universal ID's

fXiai release Text Annotations

Expressions for fXii surface activation

reaction rate

J

((Kf * fXiib) - (Kr * fXiiba)) [molecules.um-2.s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

0.0 [1]

forward rate constant

Kf

1.0 [s-1]

reverse rate constant

Kr

0.0 [s-1]

Expressions for fXii autoinhibition

reaction rate

J

(((Kf * fXiiba) * fXiiba) - ((Kr * fXiiba) * fXiib)) [molecules.um-2.s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

0.0 [1]

forward rate constant

Kf

0.1 [um2.s-1.molecules-1]

reverse rate constant

Kr

0.0 [um2.s-1.molecules-1]

Expressions for fXii binding

reaction rate

J

((Kf * fXii) - (Kr * fXiib)) [molecules.um-2.s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

0.0 [1]

forward rate constant

Kf

0.28 [molecules.um-2.s-1.uM-1]

reverse rate constant

Kr

0.01 [s-1]

Expressions for fXiai release

reaction rate

J

((Kf * fXiiba) - (Kr * fXiia)) [molecules.um-2.s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

0.0 [1]

forward rate constant

Kf

0.0 [s-1]

reverse rate constant

Kr

0.0 [molecules.um-2.s-1.uM-1]

Structures

Name
Type
Electrical
Membrane0 Membrane c1(+)   c0(-)
c1 Compartment (+)   (-)
c0 Compartment (+)   (-)

Membrane0 Universal ID's

Membrane0 Text Annotations

c1 Universal ID's

c1 Text Annotations

c0 Universal ID's

c0 Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
C1 c0 c0
fXiib Membrane0 Membrane0
fXiia c0 c0
fXiiba Membrane0 Membrane0
fXii c0 c0

C1 Universal ID's

C1 Text Annotations

fXiib Universal ID's

fXiib Text Annotations

fXiia Universal ID's

fXiia Text Annotations

fXiiba Universal ID's

fXiiba Text Annotations

fXii Universal ID's

fXii Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
Application0 Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Spatial (2D)

Application0 Universal ID's

Application0 Text Annotations

Specifications (Species) - Application0 go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
C1 0.0 [uM] 10.0 [um2/s] c0
fXiia 0.0 [uM] 10.0 [um2/s] c0
fXii 0.09 [uM] 10.0 [um2/s] c0
fXiib 0.0 [uM] 0.1 [um2/s] Membrane0
fXiiba 0.0 [uM] 0.1 [um2/s] Membrane0

Specifications (Reaction) - Application0 go to Simulations

Name
Enabled?
fXii surface activation included
fXii autoinhibition included
fXii binding included
fXiai release included

Simulations - Application0 go to Specifications

Name
End Time
Output Options
Simulation0 1600.0

OutputTimeStep 15.0

Application0 Universal ID's

Application0 Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Geometry1877367473

(Origin: -10.0, -12.5, 0.0; Extent: 20.0, 25.0, 10.0 [um])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Volume Analytical subdomain1 5.4 [um2] c1
Volume Analytical subdomain0 494.6 [um2] c0
Surface subdomain0_subdomain1_membrane subdomain0 | subdomain1 9.146486470695088 [um] Membrane0

Events

Name Variable Rate Expression

Global Parameters

Name
Expression

Downloads

Model Format
Model Downloads
Virtual Cell Markup Language VCML File
PDF Report Report
COMBINE Archive OMEX File
SEDML SEDML File
File Format
Application Downloads
BNGL Application0.bngl
SBML Application0.sbml
Matlab Application0.m
NFSim XML Application0.xml